Altered Destinies: A Badge of Honor
by Tif S
Summary: AU: Long before Rip Hunter joined, the time masters made a decision to send young Barry Allen away as part of a plan for a new future for Gotham. Raised as a ward of the Waynes and an older brother to Bruce, Barry doesn't know what lies ahead after Bruce's parents are murdered and they meet Detective Jim Gordon. How would destiny be altered? Book 1 in the Altered Destinies series.
1. Chapter 1

_**A/N: Here with a new story, it's a crossover and the first part of a three part series. I guess it could be considered a three way crossover of sorts with the Flash Gotham and Legends of Tomorrow, although the only characters from Legends that play a role are Rip Hunter and Gideon. I have a majority of it planned out and this first book will span pre-series as well as the contents of the first season of Gotham although it will diverge some for obvious reasons.**_

 _ **Disclaimer: I own nothing but my plot idea. Gotham belongs to DC and Fox, and Flash and Legends of Tomorrow belong to DC and the CW.**_

* * *

 **Chapter One: Aberration**

The future was bleak. Upon close inspection, darkness would encroach, and be nearly beyond saving for a single hero. The process would have to be expedited. Normally, the Time Masters would not interfere with the affairs of a single city, but this destiny would intersect and create a ripple effect for a group of heroes, and have the possibility to save more than one future.

The boy's memory, and the memory of those around him were erased, false memories implanted, and the time ship's destination carefully selected. It would not be until years later that the truth would be discovered, but by then the wheels would already be turning, and reality would be set. There would be little to be done, and the future would be saved. One aberration was a fair price to pay for the council. A fair price indeed.

* * *

London 2056: The Time Masters' Chamber

"Captain Hunter, I must ask you to forget this affair. There is no need to go jaunting about, as their is no aberration in what you're reporting."

Rip Hunter stood before the council of the Time Masters, incredulous. He had seen it show up on his monitor, a hole in certain events. Reality itself was shifting. "There is an aberration. It's clear as the nose on your face. Something is wrong. I'll investigate it myself if I have to."

"Captain Hunter, if you continue with this current course of action, I'm afraid your membership among the time masters is null."

And so it would be. That very same evening, Rip Hunter broke into the hangar and took his time ship.

"Gideon…set a course for the aberration, the year 2000 Central City"

"Captain Hunter, are you certain about this?"

"Set a course Gideon."

"Yes Captain."

Rip Hunter soon found out what the aberration was, the existence….or lack of...of Bartholomew Henry Allen.

"Have you found the aberration Captain?"

"Yes….yes I have Gideon. What information do you have about Bartholomew Henry Allen?"

"There is no public record Captain, it is encrypted. There is however, a Bartholomew Allen Wayne. Would you like me to pull the information?"

"Yes Gideon, all of it if you please decrypted." Rip Hunter sighed. This was not good at all. "Back it up to the hard drive as well, and set a course for Central City, the year 2007."

"Yes Captain, beginning decryption process now."

Central City 2007: STAR Labs

The jump was made without incident, and the Waverider managed to land cloaked upon the STAR Labs building before trouble ensued.

"Gideon," There was no response from the AI. In fact, the entire ship was eerily silent. Rip walked over to the controls. "Gideon, what is the status of the decryption?"

Silence.

"Odd." Rip Hunter leaned over the monitor and noticed the small print. _Decryption process complete, system failure. Set computation and piloting to manual?_

Rip Hunter cursed as he keyed in the confirmation, pulling up the files and backing them to a portable drive. As he read through them, he was even more convinced. This had to be resolved. He exited the ship and began pacing.

"Bollocks, what next, what to do…"

"Hey! What are you doing up here?" A gentleman around his age came out onto the roof through a door he hadn't noticed before.

Rip stopped mid pace and turned around. "Erm...yes hello. I'm new in town. Are you by any chance hiring on?"

Earth 26: Gotham City Eight years Before the Wayne Murders

Thomas Wayne felt like he had good senses. As he weaved through the streets, he knew he was being followed, so when he turned and saw a twelve year old boy reaching his hand for his coat pockets, he couldn't say he was surprised.

"Say, Kid…"

The boy stumbled backwards grunting as he fell onto the pavement in his attempt to run. "I...I can explain."

Thomas reached out a hand. "Easy Son. How about a hand up?"

The boy wrinkled his nose as his gaze dropped to Thomas' hand. He nodded and grabbed the man's hand as he was lifted to his feet and subsequently released although the man didn't remove his hand from his shoulder.

"T...thank you Mister…"

"Thomas Wayne." Thomas introduced himself proffering his other hand as he studied the boy. He wore a ratty hoodie bright red, and his white shirt was yellowed with age and time, his head covered with the hood, but his eyes held fear and wariness as his right hand remained in his pocket. Clearly this was a boy who was not entirely well off.

The boy's eyes widened anew as he pulled his hand from his pocket splaying it open. He was hysterical. "Mr. Wayne...I...please don't call the cops. Please…I didn't actually steal anything! I can't go upstate."

Thomas sighed. Well...there was one option. "I'm afraid, I'm going to have to take you to the station just for a moment while I make a phone call."

The boy ducked his head. The station...that wasn't much better.

* * *

"Name." Barry already knew he didn't like this guy. He smelled like beer, and he was chewing gum. It was disgusting.

"Barry."

"Full name kid, I got an overflowing docket. And you ain't on it. If it weren't for the fact you got mixed up with a Wayne, you'd be locked in that cell over there. So what's it stand for?"

"I don't got one, and I didn't steal anything..." Barry rolled his eyes.

The officer scoffed. "That's a riot."

"It's the truth Officer."

"First name, Bartholomew." The officer raised his eyebrows as he scratched down the name.

Barry frowned. He never said Bartholomew. This officer was crackers, filling space just for his stupid file.

"What about the rest?"

Barry shrugged. "Allen I guess."

"You guess? Middle or last?"

Another shrug.

"For God's sake." The officer snarled as he stood from his seat reaching over the table. Barry flinched back.

"Is there a problem Officer?" Barry felt a hand on his shoulder as he looked up to see Thomas Wayne behind him.

"Not at all Mr. Wayne, the kid just needs a bit more pushing."

"Give me a minute with him." Thomas' expression didn't change, but there was slight glint of steel in his eyes.

"O...of course Mr. Wayne." The officer shot out of the chair.

* * *

 ** _A/N: Chapter Two will involve Barry's chat with Mr. Wayne as a deal is reached with the Commissioner for young Barry's safety, and Barry officially meets Martha, Alfred and Bruce as back in Central City 2007, Rip Hunter meets two of our favorite trio and Harrison Wells._**


	2. Chapter 2

_**A/N: So...long time, haha...that's an understatement huh? Yeah... Well, I was recently working through catching back up on Gotham or at least starting to as far as prepping for my holiday binge of the rest of the series as well as season 4 of the Flash that I should hopefully be able to catch up on soon (around mid December is the goal, fingers crossed) as well as seeing the Justice League Trailers all over TV (Awesome am I right?), and I was looking through my notes for this story and series, and figured I should jump back in. Anyway...yeah... as usual I do not own Gotham, that belongs to FOX and DC, I do not own the Flash or Legends of Tomorrow, belongs to the CW and DC. I only own my convoluted plot.**_

* * *

 **Chapter Two: The Moment that Changes Things**

Earth 26: Gotham City Police Department

Barry knew of the Wayne family. Everyone knew of the Wayne family. They were the richest diddies in Gotham City after all, basically owned everything at least in name; in other stuff well that belonged to the underground, Maroni, Falcone and crew, but the point was the Waynes were important, and you didn't mess with important people. Not if you wanted to keep your head attached to the rest of you. He'd had a...temporary lapse.

"Barry was it?"

Barry nodded wordlessly.

"Well, Barry, you made quite the racket around here."

He shrugged.

"Look at me Son." Barry saw Thomas Wayne lean forward, moving his gaze upward at the man's words. "You seem like a smart young man, good head on your shoulders."

Barry raised his eyebrows. "How do you know?"

Thomas splayed his hands out on the table. "I don't."

"So, why are you saying it?" Barry challenged. "You shouldn't say something you don't know." He then thought better of it averting his gaze. "What I mean is Sir...I…" _Crap._

Barry was waiting for the man to stand up, to leave, to call that stupid drunk cop back to put him in his place, throw him in a cell, something other than what actually happened. What actually happened was that Thomas Wayne began to shake with silent laughter that grew gradually less silent so that it caused Barry to squirm. Wasn't he supposed to be in trouble?

"That is how I know." Mr. Wayne said. "That is exactly how I know."

"I don't...I don't understand Mr. Wayne." Barry glanced up then back down.

"Eyes up." Mr. Wayne placed a hand on Barry's shoulder causing him to flinch. "Always. Understand?"

Barry said nothing, but kept his eyes locked onto the man's. Every instinct was on alert. He was waiting for the other shoe to drop, so looking directly at Thomas Wayne, well it electrified every muscle.

"Barry,"

Barry blinked then bit his lip before he spoke. "Sir?"

"Do you have somewhere to go?"

Barry didn't answer for a long while. Somewhere to go? Barry knew what that meant, and he didn't know how to answer. Somewhere to go, well that meant a home with parents. Barry had never known his. He knew he must have had them at some point. Everyone did, but whatever vague notion of the set of people that were supposed to be parents he was supposed to have, the only image that came to mind was the lady at the shelter, the shelter where he could barely get a scrap, and he was always looking over his shoulder. He'd left that place. There were enough kids there, too many actually, and the place was a dump on stilts, like a breeze could blow it apart. He felt like he was in the way, and no one seemed to miss him, so he'd forgotten about it until Mr. Wayne asked him. Somewhere to go, well _that_ was loaded. "Maybe."

"Maybe?"

"Yeah, maybe."

"Is it a yes or a no?" Mr. Wayne said. "Maybe is not an answer Son."

Barry scoffed. "Yes it is."

Thomas Wayne didn't respond forthwith. He rose from the chair. "Consider your answer. I have to make a phone call, and then we will finish this discussion."

Barry watched the man go through a door labeled _Captain._ He watched the way the officers and detectives Thomas Wayne passed seemed to change their behavior, stood a little straighter, spoke a little less abruptly, the works. It left the boy dumbstruck. He never imagined that he would actually get to see such a shift. Far as he'd always known, people were just mean and that's how they got respect. But Mr. Wayne didn't seem mean, he wasn't sure he was actually nice either, but he didn't seem like a mean person. Yet people changed when he walked by. It was fascinating.

He wondered what Mr. Wayne was actually doing on the phone in the captain's office. There was so much that had happened in just an afternoon. He had a conversation with one of the most important people in Gotham City, and he hadn't talked to him like a rat in the gutter. That was weird. But not unwelcome. Especially since it meant he didn't have to inhale secondhand stale beer. The one question Barry still had as he waited circled his brain in a strange haze. _What happens now?_

* * *

Central City STAR Labs 2007

"Hiring on?" The man arched an eyebrow as he appraised Rip. "Well that depends on your definition."

Rip nodded. "What is yours?" He decided it was worth a shot.

"We're short staffed, and when I say short staffed…" The man chuckled. "I mean there are only five of us, one of whom is seven years old, and two of whom just started last week?"

"Really?" Rip said. "So it's only you lot then?" That was a small staff.

"Just wait one second." The man said. "Before we go any further, just who am I talking with?"

"Oh, well, yes of course. Sorry." Rip thought about it. He couldn't give his name, not his time master name anyway. "I'm Michael, Michael Hunter. And you are?"

"Dr. Harrison Wells, it's nice to meet you Michael."

"It is a pleasure Dr. Wells." Rip said.

"Well, if we are sitting down for an interview, you'd better come in." Wells said.

The building was certainly impressive. Much could be done to make STAR Labs successful, but as it stood, well it was a skeleton. It was clear that the lab was far from fully founded. If Rip was correct in his knowledge of STAR Labs, it would be another three years at least before plans for the infamous particle accelerator that had given Bartholomew Henry Allen his abilities in the unfuddled timeline was even in the development stages, and another three after that before it was operational. The equipment was certainly there. There was enough here to perhaps perform side repairs to the Waverider if he was discreet, but it would take time, time that he would have to use wisely.

"So this is STAR Labs?" Rip said.

"You've heard of us?" Dr. Wells said. He pushed the elevator button, going down.

"Certainly, I've done some research you know. Your thesis on atomic particle manipulation is certainly something Dr. Wells."

"I'm impressed. But if you've really looked into things as much as you claim then you _know_ we're barely more than a warehouse with a few interns."

"Don't be ridiculous. Why you could change the world." Rip said. "With your theories…"

"That is the hope Mr. Hunter." Dr. Wells replied. "That certainly is the hope." He looked at the man as they exited the elevator. "So this is our primary base of operations."

The "base of operations" as Wells called it, was the basement of the facility, and seemed, as far as Rip could tell, to be as much a multipurpose room or center as he'd seen thus far. They was a bank of computers in the center of the room, several screens set up with a variety of diagrams and a dry erase board with half completed and fully completed physics equations alike, doors that led to several offices, within one he saw a couch and several baubles and half finished technowhatsits, what appeared to be a medical facility, and just an overall mess of what could be considered mad genius or... erratic chaos with no defined purpose.

"Dr. Wells, I don't think I quite have the specs for the-whoa!" Rip saw a young man enter the main space tripping over his half tied shoelaces and ramming into one of the wheeled chairs, which then proceeded to ram directly into Rip's abdomen as the younger gentleman lost his footing. "Atomic...stabilizer…right." He managed to grunt out.

"Are you quite alright?" Rip had straightened himself out holding his stomach for a brief moment before he crouched down to assess the young man's condition alongside Harrison Wells whom had appeared beside them sometime during the chaos.

"Mr. Ramon, please for the love of god, watch where you're going." Dr. Wells said.

"Just a bruise. Give a man some space will you?" Mr. Ramon gave a cockeyed grin. "Sorry Dr. Wells, won't happen again Capitan." The young man saluted as he stood, but then he nearly buckled under the strain of what Rip thought was a twisted ankle.

"Cisco," Dr. Wells groaned. "Sit down while I find Miss Snow."

Rip obliged the man who seemed altogether harried as he left muttering under his breath, by taking the offending chair and pushing it nearer, before he helped Cisco Ramon to his feet and into said chair. "I would advise you heed his advice."

"Which part?" Cisco replied.

"Both would be preferable, but that's just a guess." Rip said.

"Oh," Cisco snapped his fingers. "By the way man, who exactly are you? I'd like to know who I nearly killed so I can apologize properly." The grin was still in place.

"You have a tendency to exaggerate correct?" Rip raised his eyebrows. "You seem the type." Rip then pulled over a small table which he propped Cisco's leg onto.

"I resent that." Cisco scowled, but it didn't last long. "But you're probably right."

"Michael," Rip said. "Michael Hunter."

"Nice to meet you Mike, sorry I kinda mauled you with the chair." Cisco said.

"Michael." Rip said. "My name is Michael."

"That's about as boring as Harrison." Cisco said. "We all call Dr. Wells Harry, so I'll start calling you Mike."

"Please don't, really that's not necessary, I quite enjoy my name as-. Rip started to speak but was interrupted.

"So, Mike," Rip sighed loudly closing his eyes in annoyance as Cisco began speaking "I'm Cisco. I'm the resident engineer around here, anything tech, I got your back dude."

"That's good to know, thank you." Rip said.

"So, you're joining the team?" Cisco asked.

"I suppose, though it might remain to be seen. Dr. Wells is interviewing me."

"Interview…" Cisco laughed. "Pssh...Wells interviews by letting you do. So you're already in."

"Well, that's brilliant." Rip smiled. If what Cisco said was true, it would make it easier to sort out what to do, and find out more information about his new companions. Getting Gideon back online was probably the first thing he should attempt. The ship, well staying in Central City was the best course of action. The ship could wait a bit longer. And having a position in STAR Labs, it would make finding allies, and information that much easier. The two he met so far seemed as though they could be helpful. He had definitely hit upon a stroke of luck landing here.

* * *

 _ **A/N: Alright, so this will be a long one. I apologize. A few things about this story that could be helpful going forward. Just some technical what have you and for your information if you're interested in that sort of thing. If not, feel free to skip it and go to the bottom. :)**_

 _ **As far as the Flash goes, well, as established, Barry does not exist on this Earth (Earth 1) due to being placed in Gotham on Earth 26 by the time masters. He was taken from Earth 1's timeline, so that changes a few things regarding Harrison Wells. This Harrison Wells is technically, for all intents and purposes the original Wells from the "original" timeline without Thawne's interference, but I've taken several liberties and combined a few things. As Barry does not exist, Eobard Thawne does not take over Wells' life, however, Jesse Wells will be involved in the story so I suppose Wells is in a sense a bit of a hybrid version of himself and Harry from Earth 2. And the timeline will still be accelerated to match the show's as far as years go.**_

 _ **As far as Gotham and the players for that goes, well I set the start of the story pre-series so we will not see Thomas and Martha out of the picture just yet. As this is based on both television verses, there is a juxtaposition that I'm quite sure will be entertaining. Rather than Bruce being older than Barry which is normally or well close to normally the case in other contexts as far as I know, Barry is older than Bruce here by about eight years or so. Being that this is on different Earth, things work a bit differently. The meeting that is accelerated is of course the meeting that we know as the formation of the Justice League, which is as I'm imagining it in this verse a bit more timey wimey. Think Barry meeting Supergirl meets invasion crossover, Earth jumping and all that good stuff.**_

 ** _Well I hope you enjoyed this FYI, and if you are interested in knowing a bit more about a few key players, check out my polyvore collection for the Altered Destinies AU which you can find here. (Just remove the spaces and click on the Collection called Altered Destinies AU)_** _ **tiffster-1. polyvore**_

 _ **Let me know your thoughts, predictions and suggestions. I'd love to know.**_


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